{"id":3309,"date":"2019-05-17T11:15:37","date_gmt":"2019-05-17T10:15:37","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=3309"},"modified":"2019-05-17T11:17:29","modified_gmt":"2019-05-17T10:17:29","slug":"fasta_number","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/fasta_number\/","title":{"rendered":"Fasta_number"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>A number of python scripts are provided by this installation. The following information came from the maintainers webpage:<\/p>\n<p><code>fasta_number.py<\/code> &#8211; Replace FASTA labels with xxx1, xxx2, xxx3 etc, where xxx is a prefix provided as a commend-line argument. Used e.g. to label OTUs as OTU_1, OTU_2 etc.<\/p>\n<p><code>fastq_strip_barcode_relabel.py<\/code> &#8211; Strips barcode and primer, adds barcode sequence or barcode label to read label.<\/p>\n<p><code>faqual2fastq.py<\/code> &#8211; Converts from FASTA + QUAL format to FASTQ.<\/p>\n<p><code>uc2otutab.py<\/code> &#8211;  Converts .uc output file from mapping reads to OTUs to an OTU table in tabbed text format.<\/p>\n<p>No version number was available for the scripts, so the install date 02jun2015 has been used to distinguish them from future installs.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>No license information was available at install time.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must load the modulefile:<\/p>\n<pre>\r\nmodule load  python\/fasta_number\/02jun2015\r\n<\/pre>\n<p>This loads anaconda python suite 3.6.5 for you.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run fasta_number (and associated scripts) on the login node. It should be used within batch jobs.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Coming soon.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>These scripts are not suitable to parallel processing. If you wish to run many similar serial jobs then please use an <a href=\"\/csf\/csf-user-documentation\/sge-job-arrays\/\">SGE job array<\/a>. <\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/drive5.com\/python\/summary.html\">Drive5 Python Scripts Docmentation<\/a>.<\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>Installed on CSF3 17-May-2019.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview A number of python scripts are provided by this installation. The following information came from the maintainers webpage: fasta_number.py &#8211; Replace FASTA labels with xxx1, xxx2, xxx3 etc, where xxx is a prefix provided as a commend-line argument. Used e.g. to label OTUs as OTU_1, OTU_2 etc. fastq_strip_barcode_relabel.py &#8211; Strips barcode and primer, adds barcode sequence or barcode label to read label. faqual2fastq.py &#8211; Converts from FASTA + QUAL format to FASTQ. uc2otutab.py &#8211;.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/fasta_number\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":7,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-3309","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3309","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=3309"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3309\/revisions"}],"predecessor-version":[{"id":3311,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3309\/revisions\/3311"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=3309"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}