Count of each sequence length from a fasta file with header using len function of python

Question

I have a fasta file with 18 sequences inside. I want to extract the length of each sequence with header using the len function. My file looks like:

>DR-1
ATGTATGAGGGCAAGAAGACGAAGAACATGTTCCTGACCCGGGCCCTGGAGAAGATTCTG
GCCGACAAGGAAGTGAAGAAGGCGCATCACTCCCAGCTGCGCAAAGCGTGCGAGGTGGCC
CTAGAGGAAATAAAAGTTGAAACTGAGAAACAAAGCCCTCCTCATGGAGAAGCAAAAGCT
GGATCAGGCACCCTTCCACCAGTGAAATCAAAGACAAATTTTATTGAAGCAGACAAGTAC
TTTTTACCCTTTGAGTTGGCATGCCAGTCCAAATGTCCCCGCATAGTTAGTACATCTCTA
GATTGTTTGCAGAAACTTATTGCTTATGGGCACTTGACTGGCAGGGCTCCAGATAGTACG
ACACCAGGCAAAAAATTAATTGATAGAATTATTGAAACAATATGTGGCTGCTTCCAAGGT
CCTCAAACAGATGAAGGAGTTCAGTTGCAGATAATAAAGGCTTTACTTACCGCAGTGACA
TCACAACACATAGAAATCCATGAAGGAACTGTGCTGCAAGCTGTGAGGACATGCTACAAT
ATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTCAA
ATGCTGAACGTTATCTTTGCACGCATGGAAAACCAAGCATTACAGGAGGCCAAACAAATG
GAAAGAGAAAGACATCGGCAGCAGCAGCATTTGTTACAGTCTCCAGTAAGCCATCATGAG
CCCGAGTCACCTCATCTTAGATATTTGCCACCTCAGACTGTTGATCATATAAACCAAGAG
CATGAAGGGGATCTTGAGCCCCAAACACATGATGTGGATAAAAGTCTCCAAGATGATACA
GAGCCTGAAAACGGATCTGATATTTCCAGTGCAGAAAATGAACAGACAGAAGCTGATCAG
GCAACTGCAGCTGAAACATTATCTAAAAATGATATCTTGTATGATGGAGACTATGAAGAA
AAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGGTGAACATCATTGTTGGAGAC
ATGGGAGAAGGGATGGCTATCAGTGCAAGTACAGAAGGCAACACTGGAACTGTAGAAGAT
GGTAGTGACAGTGAAAACATCCAAGCAAATGGAATCCCAGGAACACCCATTTCTGTTGCA
TATACACCATCGTTACCTGACGACAGGTTATCTGTCTCCTCCAATGATACTCAGGAATCT
GGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAGGATGCC
>SK-1
TTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCA
GATCCAAAGTCTCATGAGTTACGGTCCAAGATTCTTTCATTGCAGTTGCTTCTGTCCATT
CTGCAGAATGCAGGACCTGTTTTCAGGACAAATGAGATGTTTATTAATGCTATCAAGCAG
TATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTTGAGCTT
TCTCTTTCCATATTTCTTACTTTGTTGTCAAACTTCAAGACACATCTGAAGATGCAAATT
GAGGTATTCTTTAAAGAAATCTTCCTGTACATTTTGGAAACGTCTACAAGCTCATTTGAC
CATAAGTGGATGGTTATTCAGACACTGACAAGGATCTGTGCAGATGCTCAGAGTGTGGTG
GACATTTATGTAAATTATGACTGTGACCTAAATGCAGCAAATATATTTGAAAGACTAGTA
AATGACCTGTCGAAAATTGCCCAAGGAAGGGGCAGCCAAGAACTTGGTATGAGTAATGTT
CAGGAATTGAGCCTGCGAAAAAAGGGGTTAGAATGTTTAGTTTCAATTTTGAAATGTATG
GTTGAATGGAGCAAGGATCAGTATGTGAACCCCAACTCTCAAACTACCCTTGGTCAGGAA
AAACCCTCAGAGCAAGAGATAAGTGAAGTTAAACACCCAGAGACTATAAACAGATATGGA
AGTTTAAACTCCTTAGAATCCACATCATCATCAGGAATTGGCAGCTACAGTACACAGATG
TCTGGCACTGATAATCCAGAACAATTTGAGGTCCTAAAGCAGCAAAAAGAAATAATAGAA
CAAGGGATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAA
GGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTA
GACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATG
>SC-1
TATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTTGTTTCAGCTCTTCGTCTA
TTTCTGGAAGGATTCCGGCTTCCAGGAGAAGCTCAGAAAATTGATCGATTAATGGAAAAA
TTTGCTGCAAGATACCTAGAGTGCAACCAAGGACAAACCCTTTTTGCTAGTGCAGATACT
GCTTATGTTTTGGCCTACTCAATTATCATGTTGACTACAGACCTTCACAGTCCACAGGTT
AAAAACAAAATGACAAAAGAACAGTACATTAAAATGAATCGTGGTATCAATGACAGTAAA
GATCTCCCTGAAGAGTATCTATCAGCCATTTATAACGAAATAGCTGGGAAAAAAATATCA
ATGAAAGAAACAAAAGAACTAACAATCCCTACAAAGTCAACTAAACAGAATGTAGCCAGT
GAAAAGCAAAGACGACTTCTGTATAACTTAGAAATGGAACAGATGGCCAAGACGGCTAAA
GCACTCATGGAAGCTGTGAGCCATGTTCAGGCACCTTTTACAAGTGCAACACACTTGGAG
CACGTGAGGCCGATGTTTAAGTTGGCTTGGACACCTTTTCTGGCTGCATTCAGTGTGGGT
CTCCAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTGCT
ATCAGGATTGCATGCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAGCACTA
GCCAGATTTACCTTACTTACAGTGAGTTCTGGTATTACTGAAATGAAACAGAAGAATATC
GACACAATAAAAACACTCATCACGGTGGCTCACACTGATGGAAATTATTTAGGAAATTCG
TGGCATGAGATCCTGAAGTGCATCAGTCAGTTAGAGCTGGCACAACTTATAGGAACTGGA
GTGAAGCCTCGGTACATTTCTGGGACTGTGAGAGGCAGAGAAGGGTCTCTCACTGGGACA
AAAGATCAGGCTCCAGATGAATTTGTTGGTCTAGGGCTAGTTGGAGGAAATGTGGACTGG
AAGCAGATAGCCAGTATTCAGGAGTCTATTGGAGAAACCAGCTCTCAAAGTGTGGTAGTT
GCTGTGGATAGAATATTCACCGGATCCACAAGGCTAGATGGAAATGCTATTGTTGATTTT
GTCCGTTGGCTATGTGCTGTGTCTATGGATGAATTGCTTTCTACTACACACCCAAGAATG
TTTAGTCTACAAAAAATAGTAGAAATATCATACTATAACATGGGAAGAATAAGACTGCAG
TGGTCTCGGATTTGGGAAGTTATTGGAGATCATTTTAATAAGGTTGGTTGCAATCCTAAT
GAAGATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAG
>SC-2
AAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATA
ATGAAACGAAACAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATG
GTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCAT
CTAGCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCAC
ATTGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCA
GTGAAGTGTTTGTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCA
ATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAG
TACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTC
CCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGG
GGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGG
TGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAG
CAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGT
GATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCC
CAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGC
TTAGAAAACGTGGTTATTCTGAATGGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACG
TGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGT
>TA-1
CCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGAT
GCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAAGATCTTCAGATAAC
AGACAGCAAGCACCACTGGTTTCTGTTTCTACTGTGAGTGAAGAAGTTAGCAAAGTGAAA
TCCACAGCAAAATTCCCAGAACAAAAATTGTTTGCTGCCCTGTTGATTAAATGTGTTGTG
CAGCTGGAACTCATCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAG
GAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTT
GATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTG
GACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGG
ACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAAAACAGGAG
ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
TACCCTCTCTTATGTGAAATTATGCAATTTGACTTGATTCCGGAACTGCGTGCTGTTCTT
AGAAGATTTTTCCTGCGAATTGGAATAGTATTTCAAATATCACAACCACCTGAACAGGAA
CTTGGGATAAACAGGCAATGA
>DR-2
ATGCAGCCACCACCTCAGGCAGTCCCGTCTGGGGTGGCTGGACCACCCCCAGCTGGGAAT
CCTCGGAGCATGTTCTGGGCCAACAGCCCTTACAGGAAGCCAGCCAATAATGCACCAGTG
GCTCCCATAACACGCCCATTGCAGCCAGTAACGGATCCGTTTGCTTTTAATAGACAGACT
CTTCAAAACACACCAGTAGGAAGTTCATCCAAAAGCAGCCTGCCCAATTTGCCTGGCCCA
GCCCTCTCTGTTTTTTCTCAGTGGCCTGGTTTGCCTGTGACTCCCACAAATGCTGGGGAT
AGCTCCACAGGATTGCATGAGCCTCTGTCAGGAACTCTGTCACAGCCTAGAGCAGATGCC
AGTCTATTTCCTCCTGCATCTACCCCTTCTTCACTCCCTGGGCTGGAGGTGAGCAGGAAT
GCTGAGGCTGATCCCAGCTCAGGACATGAAGTCCAGATGCTGCCACATTCAGCTCACTAC
ATTCCAGGAGTGGGTCCTGAGCAGCCTCTCGGGGGCCAAATGAATGACAGTGGGTCCGGG
CCTGACCAACCCATGAATAGGCATGCCCCCCATGATGGTGCCGTGACCCACGCAGCATCT
CCTTTCCTCCCTCAGCCACAGATGCCAGGTCAGTGGGGGCCTGCACAAGGAGGCCCTCAG
CCCTCCTATCAGCATCACTCACCCTACCTGGAGGGACCTGTTCAGAACATGGGGCTCCAG
GCTGCCAGCTTGCCCCATTTTCCCCCTCCATCTAGTCTACACCAGGGACCTGGCCATGAG
TCTCATGCCCCACAAACATTTACTCCAGCATCCTTGGCCAGTGGTGAAGGGAATGAGATA
GTTCACCAGCAAAGTAAAAATCACCCATTGAGTAGCTTCCCCCCTAAACACACTTTTGAG
CAGAATTCCAGAATTGGGAATATGTGGGCAAGCCCAGAGTTGAAGCAGAATCCGGGAGTG
AATAAAGAGCATCTGCTAGACCCTGCCCATGTCAATCCCTTCACTCAGGGAAATAGTCCT
GAAAACCAGGCGCATCATCCCCCAGTGGCAGCAACTAACCATGCCCTGCAAGAAGCAGCC
TCTGGAGCTCTCTCAATGTTTTTTCAAGGGGAAGAGACAGAGAATGAGGAAAATCTCTCA
TCTGAAAAAGCAGGCCTCGATAAGAGATTGAACTTGGATAGCTTTTCTTCTACCTCCAGA
CTGGGCCATCCACCACCACCTGGAGCTAGTGGTGTCTACCAGGCCTTTCCTAGAGGCCCT
AGCAGTGAGGCTGCGCAGGAAGGAGATGCGCAACCTTATTTTTCGCAGTCTGTGGGCGTC
CGTCTTGACAAACAGAGCACTGTGCCCCCTGCTAATGATGCATGGGGTGATGTTCCGGGG
ACCGGGACCCGCTGTGCCAGTGGGCCACAGTGTGAGAATGTTGAGAACTTAGAATTTGTT
CAGAATCAAGAAGTTTTGCCCCGTGAGACCCTGAGTGTGGATCCCTTCCCCCTGAGTGAT
CAGATCCGATATGGGCCCCTTCCTGGGCCAGCTGCCTCCAGGCCTGCTACTGTGGGCCTC
ACCAGAGGTGGGGGGCTAAATCTTGAGGCCCCAGACACACCACTGCACCCTACACGACCT
GACAGTGTGTCATCCAGCTACAGCAGCCATAGCCACAGAAGTCCTCCTGGGTCAGCCAGA
CCCCAAGAATTGGTGGGCACATTCATTCAGCAAGAAGTTGGGAAACTTGAAGATGATACT
TCAGGGAGTTTTTTTAAGCAAATTGATTCTTCTCCTGTTGGAGGTGAAACAGATGAGGTG
ACTGGGAGCCAAAATTGCTGCAGCAGTCTGTCCCAGCCTTCAACCCCAAGCCCTCCAAAA
CCTACAGGAGTATTCCAAACAAGTGCAAACAGTTCTTTTGAGCCAGTAAAATCCCACTTG
GTTGGAGTGAAACCAGTTGAAGCAGATCGTGCCAACATGGTGGTTGAAGTGAGAGGGACC
CAATACTGTCCGAAGAAGCGCAGGGCAGCTGTTGCACCACCTGATGCTACCTCAGGAAAC
CTGGAACAGCCACCAGACAACATGGAGACCCCGTGTGCACCTCAGGCCTGCCCTTTGCCT
CTTAGCACCACTGGAGAGGCTGGGCAACTGGTTTCAAACACGGCAGGGACACCCCTGGAT
ACTGTGCGCCCAGTGCCTGATAAGAGGCCCTCAGCCAGGGCCCAGGGACCTGTGAAGTGT
GAGAGCCCAGCAACAACTCTGTGGGCACAAAATGAGCTGCCAGATTTTGGTGGCAATGTC
CTTCTAGCCCCTGCTGCCCCTGCACTTTATGTTCCTGTAAAACCAAAACCTTCAGAGGTT
GTTCATCATCCAGAAAAGGGAATGTCTGGACAGAAGGCCTGGAAACAAGGGTCTGTGCCA
>TA-2
CCTTTGCAGAACCAAGACCCTCCTGGTGCTTCTGAGAACCTTGAGAACCCTCCCAAGGTA
GGAGAAGAGGAGGCCCTTCCAGTGCAGGCAAGTTCTGGTTATGCGAGTTTGCTTTCTTCG
CCACCCACTGAATCTTTGCACAATCAACCTGTCCTGATTGCTCAGCCTGATCAAAGCTAT
AATTTGGCTCAGCCTATTAATTTTTCTGTGTCCTTACTGAATCCTAATGAGAAGAATCAG
TCCTGGGGAGATGCTGTGGTGGGGGAGAGATCCATAGTGAGCAACAACTGGGCTCTCGGT
GGTGATCCTGAAGAACGTGCTGCTCTGTCTGGAGTTCCAGCCAGTGCTGTCACTGGCGCG
TCTTTGCCTAGCAGTATCCCCCAGAATTGTGCCCCTCAAGGTTCGGGGTCTTCTGAAATG
ATTGCTAGCCAGTCTGCCAGTTGGTTGGTTCAACAGCTATCCCCTCAAACCCCTCAAAGT
CCGCATCCAAATGCAGAAAAGGGCCCTTCCGAGTTTGTTAGTAGCCCTGCTGGCAATACA
AGTGTGATGCTAGTTCCACCTGCAAGCAGTACTTTGGTTCCTAACAGTAATAAGGCAAAG
CACTCTAGTAACCAGGAAGAAGCTGTTGGCGCCCTAGACTTCACATTAAATAGAACTTTG
GAAAATCCTGTGAGAATGTACAGCCCATCTCCTTCAGATGGCCCAGCTTCTCAGCAGCCT
CTTCCCAATCATCCCAGACAATCTGGGCCTGGGCTGCATAACCAGGATCATTTCTACCAG
CAGGTAACAAAAGATGCTCAGGACCAGCATAGACTAGAAAGAGCCCAGCCAGAGCTGGTG
CCTCCTCGGCCACAGAATTCTCCCCAAGTGCCCCAAGCATCGTGTCCAGAGCCTTCAAAT
CCTGAAAGCCCACCCACACAAGGACAGTCTGAAAGCTTGGCCCAGCCACCAGCAAGTCCA
GCTTCAGTCAACACAGGCCAGCTGCTGCCTCAGCCACCACAGGCTTCCAGTGCATCCGTT
ACATCTACCAACTCCAGCCAGGCAGCTGTGCGGTCAGAGCAGCTGTGGCTACACCCACCA
CCTCCTAATACTTTTGGCCCAGCACCTCAAGACTTGGCATCCTACTACTATTACAGACCC
CTGTATGATGCCTACCAGTCTCAGTACCCTTCACCGTACCCGTCAGATCCTGGGACAGCC
TCGCTGTACTACCAGGATATGTATGGCCTGTATGAGCCTCGTTACAGACCCTATGACAGC
TCAGCATCTGCTTATGCCGAGAACCACCGCTATTCTGAGCCTGAGCGGCCCAGCTCCCGT
GCAAGTCACTATTCCGACCAGCTTGCTCCCAGGCAAGGATATCCTGAAGGATACTATAAT
TCCAAGAGTGGATGGAGCAGTCACAGTGATTACTATGCAAATTATTACTCTGGCCAGTAT
GATTATGGAGACCCCAGCCGCTGGGATCGTTACTATGGGTCTCGCCTTAGGGATCCTCGC
ACCTGGGACCGGAGGTACTGGTATGACTCTGAACATGACCCATACAGGAAGGACCACTAT
GCTTACAGTGACAGGCCTGAGAAATGTGATGATCACTGGAGGTATGACCCTCGCTTCACT
GGGAGCTTCGACGATGACGCTGAGATCCACAGGGACCCCTATGGAGAAGAAGCAGACAGA
CGCAGCATCCACAGTGAGCACTCGGCACGGAGCCTGCGCAGCACTCACAGTCTGCCCAGC
CGCCGCAGCAGCCTCAGCTCCCATTCACACCAGAGTCAGATTTACAGAAGCCACCATGTG
ACTGGCGGTTCCTTTGAGGCCCCTCATGCCCCAGGCTCATTTCATGGTGATTATGCCTAT
GGCACATATGCCAGCAATTTCAGCGGTGCCCATGGTTTTCCAGAGTACAGCTACCCTGCA
GACACCTCCTGGCCTGCTGTGGAGCAAGTTCCATCAAGACCGACCTCTCCTGAGAAGTTT
...
...
...
...

I want the output to look like :

>DR-1
1260 
>SK-1
1020
>SC-1
1380
>SC-2
960
>TA-1
921
>DR-2
2400
TA-2
>1980
...
...
...
...

I am new to learning python for molecular analysis, so am having trouble with the logic and syntax behind it. I'm looking forward to a warm response from you. Thanks again.

dachi · Accepted Answer · 2021-06-21 16:09:12Z

3

Replace "string protein sequences.fa" with "your_fasta_file.fa" and your file should be at the same path that you created your code.

import Bio.SeqIO as IO
record_dict = IO.to_dict(IO.parse("string_protein_sequences.fa", "fasta"))
for key in record_dict.items():
    print(key[0],"\n ",len(key[1].seq))

Output:

9606.ENSP00000354718 
  2817
9606.ENSP00000383118 
  191
9606.ENSP00000275364 
  381
9606.ENSP00000265563 
  404
9606.ENSP00000265717 
  418
9606.ENSP00000348461 
  211
9606.ENSP00000249071 
  192
9606.ENSP00000304283 
  192
9606.ENSP00000400175 
  193
9606.ENSP00000285735 
  193
9606.ENSP00000339467 
  191

I hope that's what you need, good luck

edited Jun 21, 2021 at 16:09

answered Jun 20, 2021 at 12:59

dachi

915 bronze badges

$\begingroup$ Thanks for you quick respone. Unfortunately i didnt have biopython in my windows and also in Linux env. I could not make it run. Can you please give the code to run with general python code? $\endgroup$
– Kishor Kumar Sarker
Commented Jun 21, 2021 at 7:06
1

$\begingroup$ You can just install it with this command: pip install biopython, if not try the code that is in the second answer $\endgroup$
– dachi
Commented Jun 21, 2021 at 14:23

Add a comment |

dachi · Accepted Answer · 2021-06-21 16:11:32Z

Don't forget to change the file name and write the valid path

with open("string_protein_sequences.fa") as file_content:
    liste=[]
    j=-1
    for seqs in file_content:
        if seqs.startswith('>'):
            j+=1
            print(seqs,lis[j])
            some=0
            i=0
        else:
            i+=1
            some+=len(seqs) 
        liste.append(some-i)
    lis=[]
    for j in range(1,len(liste)):
        if liste[j]==0:
            lis.append(liste[j-1])
    lis.append(liste[-1])

Output:

 >9606.ENSP00000354718 (AKAP13)
  2817
 >9606.ENSP00000383118 (CDC42)
  191
 >9606.ENSP00000275364 (GNA12)
  381
 >9606.ENSP00000265563 (PRKAR2A)
  404
 >9606.ENSP00000265717 (PRKAR2B)
  418
 >9606.ENSP00000348461 (RAC1)
  211
 >9606.ENSP00000249071 (RAC2)
  192
 >9606.ENSP00000304283 (RAC3)
  192
 >9606.ENSP00000400175 (RHOA)
  193
 >9606.ENSP00000285735 (RHOC)
  193
 >9606.ENSP00000339467 (RHOG)
  191

zorbax · Accepted Answer · 2021-06-21 16:58:06Z

0

you can use a dictionary as well:

fasta = {}
with open("test.fasta", "r") as file:
    for line in file:
        line = line.strip()
        if line[0] == ">":
            header = line
            fasta[header] = ""
        else:
            data = line
            fasta[header] += data

for k in fasta.keys():
    print(f"{k}\n{len(fasta[k])}")

answered Jun 21, 2021 at 16:58

zorbax

7694 silver badges11 bronze badges

$\begingroup$ It works great! Thanks. The len information has generated on the bottom row of the header. Can i put this information with the seq id using some name like: >seq1 "len=424" AATT.........................ATTT $\endgroup$
– Kishor Kumar Sarker
Commented Sep 17, 2021 at 15:12
$\begingroup$ In that case you should use fasta.items() to iterate through the dictionary: for k, v in fasta.items(): print(f'{k} "len={len(fasta[k])}"\n{v}') $\endgroup$
– zorbax
Commented Sep 17, 2021 at 18:24

Add a comment |

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