解析基因库文件(Parsing GenBank file)

基本上，一个基因库文件由基因项（由后跟其相应的“CDS”条目（每个基因只有一个像两下面我在这里展示的“基因”）公布。我想获得locus_tag VS产品在制表符分隔两列的文件。“基因”和“CDS”总是前面和后面的空格。如果这个任务可以容易地使用已经可用的工具进行，请让我知道。

输入文件：

 gene            complement(8972..9094)
                 /locus_tag="HAPS_0004"
                 /db_xref="GeneID:7278619"
 CDS             complement(8972..9094)
                 /locus_tag="HAPS_0004"
                 /codon_start=1
                 /transl_table=11
                 /product="hypothetical protein"
                 /protein_id="YP_002474657.1"
                 /db_xref="GI:219870282"
                 /db_xref="GeneID:7278619"
                 /translation="MYYKALAHFLPTLSTMQNILSKSPLSLDFRLLFLAFIDKR"
 gene            9632..11416
                 /gene="frdA"
                 /locus_tag="HAPS_0005"
                 /db_xref="GeneID:7278620"
 CDS             9632..11416
                 /gene="frdA"
                 /locus_tag="HAPS_0005"
                 /note="part of four member fumarate reductase enzyme
                 complex FrdABCD which catalyzes the reduction of fumarate
                 to succinate during anaerobic respiration; FrdAB are the
                 catalytic subcomplex consisting of a flavoprotein subunit
                 and an iron-sulfur subunit, respectively; FrdCD are the
                 membrane components which interact with quinone and are
                 involved in electron transfer; the catalytic subunits are
                 similar to succinate dehydrogenase SdhAB"
                 /codon_start=1
                 /transl_table=11
                 /product="fumarate reductase flavoprotein subunit"
                 /protein_id="YP_002474658.1"
                 /db_xref="GI:219870283"
                 /db_xref="GeneID:7278620"
                 /translation="MQTVNVDVAIVGAGGGGLRAAIAAAEANPNLKIALISKVYPMRS
                 HTVAAEGGAAAVAKEEDSYDKHFHDTVAGGDWLCEQDVVEYFVEHSPVEMTQLERWGC
                 PWSRKADGDVNVRRFGGMKIERTWFAADKTGFHLLHTLFQTSIKYPQIIRFDEHFVVD
                 ILVDDGQVRGCVAMNMMEGTFVQINANAVVIATGGGCRAYRFNTNGGIVTGDGLSMAY
                 RHGVPLRDMEFVQYHPTGLPNTGILMTEGCRGEGGILVNKDGYRYLQDYGLGPETPVG
                 KPENKYMELGPRDKVSQAFWQEWRKGNTLKTAKGVDVVHLDLRHLGEKYLHERLPFIC
                 ELAQAYEGVDPAKAPIPVRPVVHYTMGGIEVDQHAETCIKGLFAVGECASSGLHGANR
                 LGSNSLAELVVFGKVAGEMAAKRAVEATARNQAVIDAQAKDVLERVYALARQEGEESW
                 SQIRNEMGDSMEEGCGIYRTQESMEKTVAKIAELKERYKRIKVKDSSSVFNTDLLYKI
                 ELGYILDVAQSISSSAVERKESRGAHQRLDYVERDDVNYLKHTLAFYNADGTPTIKYS
                 DVKITKSQPAKRVYGAEAEAQEAAAKKE"

期望的输出（locus_tag VS在制表符分隔的2个columnfile产品）：

HAPS_0004 hypothetical protein
HAPS_0005 fumarate reductase flavoprotein subunit

事实上，具有该输出将是对于每个基因（用于仅一个基因示出）理想的，一个行：

 locus_tag="HAPS_0004" db_xref="GeneID:7278619" complement(8972..9094) codon_start=1 transl_table=11 product="hypothetical protein" protein_id="YP_002474657.1" db_xref="GI:219870282" db_xref="GeneID:7278619" translation="MYYKALAHFLPTLSTMQNILSKSPLSLDFRLLFLAFIDKR"

Answer 1:

perl -nE'
  BEGIN{ ($/, $") = ("CDS", "\t") }
  say "@r[0,1]" if @r= m!/(?:locus_tag|product)="(.+?)"!g and @r>1
' file

产量

HAPS_0004       hypothetical protein
HAPS_0005       fumarate reductase flavoprotein subunit

文章来源: Parsing GenBank file