I need to extract certain lines from a GenBank file on Linux.
Input file:
LOCUS XM_012540068 1713 bp mRNA linear MAM 11-JAN-2018
DEFINITION PREDICTED: Sarcophilus harrisii cytochrome c oxidase assembly
protein COX15 homolog (LOC100925550), mRNA.
ACCESSION XM_012540068
VERSION XM_012540068.2
DBLINK BioProject: PRJNA167725
KEYWORDS RefSeq; corrected model.
SOURCE Sarcophilus harrisii (Tasmanian devil)
ORGANISM Sarcophilus harrisii
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Metatheria; Dasyuromorphia; Dasyuridae; Sarcophilus.
COMMENT MODEL REFSEQ: This record is predicted by automated computational
analysis. This record is derived from a genomic sequence
(NW_003816462.1) and transcript sequence (GEDN01126617.1) annotated
using gene prediction method: Gnomon, supported by EST evidence.
Also see:
Documentation of NCBI's Annotation Process
On Jan 11, 2018 this sequence version replaced XM_012540068.1.
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI
Annotation Status :: Full annotation
Annotation Name :: Sarcophilus harrisii Annotation
Release 102
Annotation Version :: 102
Annotation Pipeline :: NCBI eukaryotic genome annotation
pipeline
Annotation Software Version :: 8.0
Annotation Method :: Best-placed RefSeq; Gnomon
Features Annotated :: Gene; mRNA; CDS; ncRNA
##Genome-Annotation-Data-END##
##RefSeq-Attributes-START##
assembly gap :: added 136 transcript bases to patch genome assembly
gap
##RefSeq-Attributes-END##
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-136 GEDN01126617.1 1-136
137-327 AEFK01003589.1 1071-1261
328-450 AEFK01003589.1 2007-2129
451-637 AEFK01003589.1 2869-3055
638-805 AEFK01003589.1 6071-6238
806-887 AEFK01003591.1 516-597
888-1042 AEFK01003591.1 1431-1585
1043-1156 AEFK01003591.1 4257-4370
1157-1713 AEFK01003591.1 6191-6747
FEATURES Location/Qualifiers
source 1..1713
/organism="Sarcophilus harrisii"
/mol_type="mRNA"
/db_xref="taxon:9305"
/chromosome="1"
/map="unlocalized"
/sex="female"
gene 1..1713
/gene="LOC100925550"
/note="The sequence of the model RefSeq transcript was
modified relative to its source genomic sequence to
represent the inferred CDS: added 136 bases not found in
genome assembly; Derived by automated computational
analysis using gene prediction method: Gnomon. Supporting
evidence includes similarity to: 10 ESTs, 11 Proteins, and
100% coverage of the annotated genomic feature by RNAseq
alignments, including 5 samples with support for all
annotated introns"
/db_xref="GeneID:100925550"
CDS 53..1288
/gene="LOC100925550"
/note="The sequence of the model RefSeq protein was
modified relative to its source genomic sequence to
represent the inferred CDS: added 84 bases not found in
genome assembly"
/codon_start=1
/product="cytochrome c oxidase assembly protein COX15
homolog"
/protein_id="XP_012395522.2"
/db_xref="GeneID:100925550"
/translation="MMRLLFPPLKAVLGSPGVRLQAAGGAHRCGCHYGQKLSLLQRQH
STLSEVALQSGRGAVSVPTKAAQRIMGRWLLVCSGTVAGAVILGGVTRLTESGLSMVD
WHLIKGMKPPTSQEEWEAEFQKYQQFPEFKILNHNMTLAEFKFIWYMEYSHRMWGRIV
GLAYVLPTVYFWRKGWLTHGMKGRVLALCGLVCFQGLLGWYMVKSGLEEKPDSYDIPR
VSQYRLAAHLGSALVLYCASLWTGLSLLLPRDKLPETRKLLQLRRFAHGTAGLVFLTA
LSGAFVAGLDAGLVYNSFPKMGDHWIPEDLFTFSPVLRNVFENPTMVQFDHRVLGIAT
VTAITGLYFFSRRIPLPRRAKMAVTTLLAVAYAQVALGISTLLTYVPTPLAAVHQSGS
LALLSIALWLMNELRRIPK"
ORIGIN
1 gtggggcgac cgagggaggc cgctgcgagg ctgtgacttt gagactcgcg cgatgatgcg
61 attgctgttt cctcctctga aagcggtgct gggcagtccg ggcgtccggc tgcaggctgc
121 tgggggagct caccggtgcg gttgccatta tgggcaaaag ctctctctct tgcaaagaca
181 gcacagtact ctgtctgaag tagctttgca gtctggaagg ggagcagtgt ctgtccccac
241 aaaggctgcc cagcgcatta tgggtcgttg gctcttggtc tgcagcggaa cagtagcagg
301 agcggtgatt cttggtggag tgactaggtt gacagagtct gggctctcca tggtagattg
361 gcacttgata aaaggaatga aaccacccac aagccaagaa gaatgggaag cagagttcca
421 aaaataccag cagtttccag aatttaaaat cttgaaccat aacatgacat tagcagaatt
481 caagtttatc tggtacatgg aatactcaca cagaatgtgg ggtcggattg tgggcctagc
541 atatgtcctt cccactgtct acttttggag aaagggctgg ctcacccatg gcatgaaagg
601 tcgtgttctt gccctctgtg gtttagtctg tttccaggga ctgttggggt ggtatatggt
661 gaagagtgga ttagaagaaa agccagattc ttatgacatc cctcgggtga gccagtatcg
721 tctggccgct cacttgggct ctgcccttgt cctctactgt gccagcttgt ggactggact
781 ctccctcttg cttcctcgag acaagttgcc agaaacccga aagctcttgc agctgaggcg
841 atttgctcat gggacagcag gcctggtttt ccttacagct ctttcaggag cctttgtggc
901 aggcctggat gctggacttg tatacaactc ctttcctaag atgggagacc actggatccc
961 agaagatctc tttaccttct ctccagttct tagaaatgtc tttgagaatc caaccatggt
1021 gcagtttgat catcgagtcc tgggaatcgc tacagtcaca gccattactg gactttactt
1081 cttctccagg agaatccctc ttcctcgaag ggccaaaatg gcagtgacaa cattgctggc
1141 tgtggcctat gcacaggtgg ccttgggcat tagtactcta ctaacgtatg ttccaactcc
1201 tttggctgca gttcaccagt cagggtccct cgctttgctc agcattgccc tttggcttat
1261 gaacgaactg aggcgaatcc caaagtaatg cccaggcagg tatttttctg gactcttccc
1321 aggcttttga gagctctgta gagggcatga ggcttccctc ctgttgaatt aaagaattga
1381 tgtggtagac agatcagaag atcaagaatg aagttactga tctgaggatt ctttttcaga
1441 ctaaacaaac tactcttctt ccataagttg tcacttgctt tttaatgtgc tattaagatc
1501 ccttccaact ttcactactc tgattctttt gatacagcaa taccactgat aggtctgtgt
1561 ctcagagttg ggagggaggg aaggaaaaaa aaaacttttt gtacaaacgt acaaaactat
1621 agtagttcct tttgtgggaa ctaaaataag gaaattttct ttctttttta tttattcgtt
1681 ttcaacattt acttttataa gatttagatt ttc
//
My code:
tr "\"" " " < XM_012540068.2.gb | egrep -v "/db_xref= taxon" | awk -F= '/GeneID:|(gene|product|protein_id|translation)=/{print $2}' | sort -u
What I get:
GeneID:100925550
LOC100925550
MMRLLFPPLKAVLGSPGVRLQAAGGAHRCGCHYGQKLSLLQRQH
XP_012395522.2
cytochrome c oxidase assembly protein COX15
What I want:
GeneID:100925550
LOC100925550
MMRLLFPPLKAVLGSPGVRLQAAGGAHRCGCHYGQKLSLLQRQH...(sequence goes on...)
XP_012395522.2
cytochrome c oxidase assembly protein COX15 homolog
Preferably, it has to be a mastercode for every GenBank-file. For a project I've got to loop through 78 GenBank-files, and extract the same data. I asked a similar question earlier, but the solution there doesn't work when the protein's name spans multiple lines.
