If the section starts with some wording i.e if something is written at the start of a section and which is followed by.. 1... 2.... 3.. then it will be "clause". like section 2 stats with "In this Act, unless the context otherwise requires,—"and thereafter 1, 2, 3.. are given which are "clauses" not sub section. however if you look at section 139 which is followed by sub section 1 i.e nothing is written after section 139 and sub section 1 starts just after 139, in that case it will be sub section 1 of section 139. Section 2, Section 10 all are having clauses only, no sub sections are there.
suppose
139. (1) Every person,—
(a) being a company or a firm; or
(b) being a person other than a company or a firm, if his total income or the total income of any other person in respect of which he is assessable under this Act during the previous year exceeded the maximum amount which is not chargeable to income-tax,
shall, on or before the due date, furnish a return of his income or the income of such other person during the previous year, in the prescribed form and verified in the prescribed manner and setting forth such other particulars as may be prescribed :